Metagenomic insights of antibiotic resistance genes in Laguna Lake, Phillipines through nanopore sequencing

Antimicrobial resistance genes (ARGs) in aquatic environments pose a significant threat to public health and ecological balance. This study investigates the diversity of ARGs in Laguna Lake, Philippines, using nanopore-based metagenomics and specialized bioinformatics tools. Water samples were collected in September 2023 and March 2024 from various locations within the lake. These samples underwent DNA extraction, library preparation, and sequencing with the Oxford Nanopore MinION device. Reads were processed to remove low-quality sequences and subjected to taxonomic and ARG classification using various bioinformatic tools. Taxonomic analysis revealed that Proteobacteria [September (46.87%) and March (42.02%)], Actinobacteria (17.18 to 24.44%), and Firmicutes (3.93 to 8.94%) were the dominant Phyla, showing seasonal variations in their relative abundances. ARG analysis revealed multiple antibiotic types and subtypes in the lake, with multidrug resistance genes most prevalent. Notable differences in ARG types and read counts were observed between the two sampling periods. The occurrence of these genes per phylum was also identified. The study provides insights into the impact of environmental factors, including temperature and human activities, on the microbial community and ARG dissemination within the lake, warranting further investigation. Lastly, these findings underscore the need for advanced genomic techniques and bioinformatic tools to understand and mitigate the spread of antimicrobial resistance in aquatic ecosystems.